When running transrate on multiple assemblies at the same time, it seems that transrate shares the CPU instruction across runs.
My snakemake pipeline provides 14 cores for each of 4 runs. This works with the other tools (Trinity, Shannon, trimmomatic etc) but as soon as transrate steps start only 14 instead of 48 cores are used. This is even the case when all four transrate processes are running concurrently (all shown to be running in htop).
This is slowing down performance of the whole pipeline since the transrate run is a bottleneck.
Is transrate somehow exporting a global variable that is then used? How can this behaviour be avoided?
I am running transrate v1.0.3 on CentOS 6
When running transrate on multiple assemblies at the same time, it seems that transrate shares the CPU instruction across runs.
My snakemake pipeline provides 14 cores for each of 4 runs. This works with the other tools (Trinity, Shannon, trimmomatic etc) but as soon as transrate steps start only 14 instead of 48 cores are used. This is even the case when all four transrate processes are running concurrently (all shown to be running in htop). This is slowing down performance of the whole pipeline since the transrate run is a bottleneck. Is transrate somehow exporting a global variable that is then used? How can this behaviour be avoided?
Thanks for your help, Jeremias